A man holds a Saturday copy of the newspaper with its headline which reads 'the constitution suspended' as people gathered in support outside the headquarters of the Zaman newspaper in Istanbul, Turkey, Sunday, March 6, 2016.

The editor-in-chief was fired, and hundreds of protesters calling for press freedom were hosed with water cannons and hit with tear gas through Saturday.

When the next edition of Zaman was published on Sunday, the former opposition newspaper had a decidedly pro-government slant. The front page showed President Recep Tayyip Erdoğan smiling during a ceremony to mark progress and “historic excitement” over a third bridge spanning the Bosphorus.

For media and human rights watchdogs, the closing of Zaman and its larger media group – all linked to an exiled cleric opposed to Mr. Erdoğan – is the latest of many recent setbacks to press freedom in Turkey.

But for political analysts following Erdoğan’s long-term project to create a powerful presidential system in Turkey, the takeover of Zaman was only the latest episode in a systematic crackdown on opponents of the president and his Justice and Development Party (AKP), which has ruled Turkey since 2002.

The high-profile media takeover was carried out even as senior former AKP officials have voiced concern about some of Erdogan’s actions. Prime Minister Ahmet Davutoğlu, a longtime ally and senior adviser to Erdoğan, also has been asked by party deputies about friction between the two.

“President Erdoğan knows that when he takes the offensive, he manages to rally support of the grassroots, the conservative voters of the party … so he took the offensive by seizing Zaman,” says İhsan Daği, a professor at the Middle East Technical University in Ankara.

“It is a show of strength, in fact,” says Mr. Daği. “It’s not out of weakness, but an expectation that if he appears weak, if people see that there are some opposition views developing, he thinks he may not be in a state of control if that process starts – he just wants to stop that process.”

Mr. Davutoğlu said the Zaman takeover was “a completely legal process” and that “no one should have hesitation about press freedom in Turkey.” He has rejected rumors of a personal rift with Erdoğan, whom he calls “the charismatic leader of our political movement.”

In a statement, Zaman’s English-language sister newspaper Today’s Zaman rued the “darkest and gloomiest days” for press freedom, which is “a major benchmark for democracy and the rule of law.”

Switch to Public Enemy No. 1

The media group – and four powerful businessmen arrested separately on Friday – are all linked to the cleric Fethullah Gülen, whom Erdoğan and state prosecutors accuse of creating a “terrorist” parallel state network in Turkey that twice in 2013 tried to topple the government.

Mr. Gülen lives in exile in the US and was once a close ally of Erdoğan; Zaman once lauded the AKP’s every move in its pages.

But since the falling out between the two men – Gülen's followers in the police and judiciary leaked audio recordings in 2013 that appeared to show official corruption at the very highest levels – the Gülen movement has been cast as Public Enemy No. 1.

Some pro-AKP operatives call the Gülenists in Turkey the equivalent of Al Qaeda for the United States; prosecutors have coined the term “Fethullahist Terror Organization” (FETÖ) to describe it.

“It’s like Erdoğan is confiscating everything that belongs to the Gülen movement, one by one. There’s a process,” says Mustafa Akyol, an author on Islamic issues and a columnist for Hürriyet Daily News. A similar media group was put under administration last October, immediately produced pro-government reports, and had since been dismantled.

Mr. Akyol says there are elements of revenge against Gülen in Erdoğan's crackdown. But there is also a sense that Gülen’s network poses a real threat to his leadership.

“Yes, it is true, we know that the Gülen movement really created a network in the police and the judiciary … and they used this in very aggressive ways, for witch hunts against Mr. Erdoğan’s enemies when they were allies,” he says.

That network has been turned against Erdoğan since his fallout with Gülen.

For Erdoğan, 'it's all connected'

Turkey is roiling with seemingly more severe problems, from a renewed war against the separatist Kurdistan Workers’ Party (PKK) in the southeast and the infiltration of Islamic State cells that have conducted bomb attacks, to hosting more than two million refugees from Syria.

But there is still time to systematically go after Gülenists at home, and even investigate and prosecute what the judiciary recently acknowledged to be 1,800 cases of “insulting” the president, sometimes for as little as a critical tweet.

“For them it’s all just one major battle, it’s all connected,” says Akyol. “For Erdoğan’s world view, there’s the righteous and glorious Erdoğan and his loyal supporters, and the rest is enemy territory, within the country or outside.”

“He doesn’t want to see even one single dissenting voice,” says Daği, the professor. “He knows that in this country, people really respect the powerful man. There is this culture of submission to the powerful and he plays that very skillfully.

“All other issues like Islamic State, PKK … they are all secondary,” adds Daği. “The primary issue for Turkish politics is the survival of Tayyip Erdoğan, politically.”